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BLAST query problem

BLAST query problem - DNA Forum

BLAST query problem - Discuss DNA, the molecule of hereditary. Topics include DNA structure, DNA replication, DNA function.


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Old 08-08-2011, 12:19 PM
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Default BLAST query problem



Hey guys,

sry for my probably simple question, but i got some serious problem with a certain BLAST query.

I searching for the best spots to place two opposing zinc finger nucleases in a certain gene.

Screening for the very sequences is done by ZiFiT, no problem.

eg.: CGCGACCCCNNNNNNGGCGCGGCC

The first nine nucleotids are for the first protein, then a spacer and the second protein.

Now I need to get sure, that there a few as possible other sequences in the whole genome that are the same or similiar.
I need the two nucleases be as specific as possible.

Therefore I blast the sequence.


Since these proteins need to dimerize to work, I don't care, if the first part or the second part of the sequence happen to be somewhere else isolated too.

I'm only interested if both parts, with the proper spacer in between, happen to be somewhere else too, or similiar sequences respectively.

Now blastn gives me both results.

It gives me the one I'm interested in, like that:
Code:
Score = 23.8 bits (12),  Expect =  2498
 Identities = 18/24 (75%), Gaps = 0/24 (0%)
 Strand=Plus/Plus

Query  1         CGCGACCCCNNNNNNGGCGCGGCC  24
                 |||||||||      |||||||||
Sbjct  93104646  CGCGACCCCGTCCCGGGCGCGGCC  93104669



but it also gives me the short ones, i'm not interested in, like that:
Code:
 Score = 18.0 bits (9),  Expect = 136135
 Identities = 9/9 (100%), Gaps = 0/9 (0%)
 Strand=Plus/Minus

Query  16       GGCGCGGCC  24
                |||||||||
Sbjct  1800501  GGCGCGGCC  1800493





So, basically what I need, is how to restrict the results to a certain lenght, I guess (not to a certain minimum amount of identity, but just to a minimum amount of length as a wohle).

Again, sry for my simple question, but I tried a lot, and just haven't come to an end yet.

It would be awesome if someone could give me a hint how to do that.
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